1) Backup and restore the patch using HD Edit. If there is some kind of corruption in the patch, this may help strip it out,

2) Try manually rebuilding the patch from scratch. This is obviously a pain in the back end but in the process of rebuilding you may spot the problem.

Also, when you reloaded the flash memory did you do a global settings reset also? hold down the 'left' button on the directional keypad and power up the Pod. This does a global settings reset and can help. It is also useful if the preset you were working with was corrupt as it jumps you back to patch 1A. If you use this, you will need to check your global settings to make sure they are how you want them. You will also need to recalibrate your expression pedal (details here -->http://line6.com/support/docs/DOC-2223). None of your homemade presets will be lost but your setlist names will be renamed to the default names.

The information above may not be current, and you should direct questions to the current forum or review the manual.